Structure of PDB 5m4q Chain B

Receptor sequence
>5m4qB (length=478) Species: 9606 (Homo sapiens) [Search protein sequence]
GPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQ
RYCTDTGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHA
TWMGKIHSKEHFKEKYAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSG
SVCREASFDGISKFEVNNTILHPEIVECRVFKTDMELEVLRYTNKISSEA
HREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSSYTCICGSGENSAVLH
YGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTADQKAV
YEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMV
QAHLGAVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQP
GMVLTVEPGIYFIDHLLDEALADPARASFLNREVLQRFRGFGGVRIEEDV
VVTDSGIELLTCVPRTVEEIEACMAGCD
3D structure
PDB5m4q Substrate specificity and reaction mechanism of human prolidase.
ChainB
Resolution1.73 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D60 H255 D276 D287 H366 H370 H377 E412 Y416 R450 E452
Catalytic site (residue number reindexed from 1) D55 H250 D271 D282 H361 H365 H372 E407 Y411 R445 E447
Enzyme Commision number 3.4.13.9: Xaa-Pro dipeptidase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 MN B D287 H370 T410 E412 E452 D282 H365 T405 E407 E447
BS02 MN B Y241 D276 D287 E452 Y236 D271 D282 E447
BS03 OH B E412 E452 E407 E447
BS04 PRO B H255 H366 R398 E412 R450 H250 H361 R393 E407 R445 MOAD: Ki=0.31mM
PDBbind-CN: -logKd/Ki=3.51,Ki=0.31mM
Gene Ontology
Molecular Function
GO:0004181 metallocarboxypeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0016805 dipeptidase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
GO:0070006 metalloaminopeptidase activity
GO:0102009 proline dipeptidase activity
Biological Process
GO:0006508 proteolysis
GO:0006520 amino acid metabolic process
GO:0030574 collagen catabolic process
GO:0043069 negative regulation of programmed cell death
Cellular Component
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5m4q, PDBe:5m4q, PDBj:5m4q
PDBsum5m4q
PubMed28677335
UniProtP12955|PEPD_HUMAN Xaa-Pro dipeptidase (Gene Name=PEPD)

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